Autodock Vina Software Process for Efficient Large-Scale Cognate Ligand Screening

Description:

The invention pertains to software processes, additions, and docking approaches to Autodock Vina that speeds the rate and efficiency of analyzing ligand interactions with a receptor by cognate ligands and rewards conformations in the scoring algorithm for residue interactions that are based on the biological data. The score is multiplied by a weighting factor to control the degree of ligand-residue interactions that are considered. This multiplier is then added to the docking score for confirmation. This new scoring mechanism is used to score each compound in each generation of the evolutionary genetic algorithm. This docking approach can be used to score and rank compounds in large-scale virtual screening applications. The software includes logic for converting SDF formatted to an Autodock Vina compatible format (containing approx. 25,000 compounds each) and submits the job to the portable batch system on the computing cluster to convert into PDBC files (a concatenated filed type). Modified Vina software stores the analyzed binding pocket in RAM that does not have to be recomputed upon every docking process. This increases the efficiency of the docking algorithm by several orders of magnitude. The software on the head node intelligently monitors memory usage, CPU usage and docking speed. Based on this information, the head node elastically controls the load on each node.